A couple of thoughts:
Are the engine mounts in good condition? (asking this based on the issue of noise or knocking sound when running shaft alternator)
Did the problem begin after you last filled up with fuel? If so, you may have bad fuel.
Do you have a good flow of fuel all the way from the tank to the injectors (checking filters, joints for leakage, etc all along the fuel path)
Have you bled the system to eliminate air?
With best regards,
Sailing Vessel - Cream Puff - SM2K - #275
Currently cruising - Santa Marta, Colombia
Hello fellow amelians